XMAS: crash in ~QGridLayout()

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000010d465600 (most recent call first):
  File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 110000,
  "procLaunch" : "2023-06-21 16:49:32.8822 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "procStartAbsTime" : 95037472859848,
  "coalitionID" : 1733,
  "osVersion" : {
    "train" : "macOS 12.6.2",
    "build" : "21G320",
    "releaseType" : "User"
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  "captureTime" : "2023-06-22 14:47:50.2463 +0200",
  "incident" : "7C1D0AC7-19C3-41B0-8BEF-853923174DE1",
  "bug_type" : "309",
  "pid" : 15319,
  "procExitAbsTime" : 119310809169879,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"C1084B94-4A07-53B5-9A85-2355AD82ABA3","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "19CCC37A-33D6-4584-2DD0-78BED36A390F",
  "wakeTime" : 13308,
  "bridgeVersion" : {"build":"20P2059","train":"7.1"},
  "sleepWakeUUID" : "0FC073BC-8DEC-484B-AD43-1BAE1D3312B5",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4369485824\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104711000-104712000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4369485824\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104711000-104712000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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  "faultingThread" : 0,
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    "size" : 3096576,
    "uuid" : "06fdecd6-9f69-397b-b1e2-a8226c0ba7ed",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703380881408,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15269888,
    "uuid" : "af3d9501-0abf-3c79-955c-c42c29af6351",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4374306816,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4369485824,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4517154816,
    "size" : 442368,
    "uuid" : "b53641ea-6cd4-39c9-9b14-59c92cfd9584",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4517908480,
    "size" : 64028672,
    "uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4987113472,
    "size" : 165052416,
    "uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5198516224,
    "size" : 147456,
    "uuid" : "9a744198-7fb3-3c4f-b935-3646fa131615",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so",
    "name" : "interpreter.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5741604864,
    "size" : 63373312,
    "uuid" : "ccf8b470-9ccf-3558-9748-04374e88d1ea",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
    "name" : "libopenblas.0.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703332773888,
  "size" : 19331678208,
  "uuid" : "3172f8f5-c412-3210-95e0-1cfd89e01f8a"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=5.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 8600K        9 \nCG image                           196K       26 \nColorSync                          232K       28 \nCoreAnimation                      140K       21 \nCoreGraphics                        20K        4 \nCoreServices                       248K        1 \nCoreUI image data                 3696K       41 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             3.4G      372 \nMALLOC guard page                   48K       10 \nMALLOC_MEDIUM (reserved)           1.3G       16         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        2 \nObjC additional data                15K        1 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        172K       43 \nStack                            164.8M       44 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      316.7M      280 \nVM_ALLOCATE (reserved)           384.0M        4         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            62.7M      831 \n__DATA_CONST                      32.7M      343 \n__DATA_DIRTY                      1641K      213 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       696.9M      282 \n__TEXT                           929.7M      810 \n__UNICODE                          592K        1 \ndyld private memory               1280K        3 \nmapped file                      189.2M       50 \nshared memory                     3036K       35 \n===========                     =======  ======= \nTOTAL                              7.6G     3486 \nTOTAL, minus reserved VM space     5.8G     3486 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "6112e14f37f5d11121dcd519",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "634710168e8be655c1316aaa"
      },
      "deploymentId" : 240000231
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
      "experimentId" : "6317d2003d24842ff850182a",
      "deploymentId" : 400000013
    }
  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes1/cryosparc_P197_J770_map_sharp.mrc"

Opened cryosparc_P197_J770_map_sharp.mrc as #1, grid size 300,300,300, pixel
0.84, shown at level 0.00718, step 2, values float32  

> surface dust #1 size 8.4

> volume #1 step 1

> volume #1 level 0.008817

> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes2/cryosparc_P197_J776_005_volume_map_sharp.mrc"

Opened cryosparc_P197_J776_005_volume_map_sharp.mrc as #2, grid size
450,450,450, pixel 0.84, shown at level 0.134, step 2, values float32  

> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes2/cryosparc_P197_J781_006_volume_map_sharp.mrc"

Opened cryosparc_P197_J781_006_volume_map_sharp.mrc as #3, grid size
450,450,450, pixel 0.84, shown at level 0.098, step 2, values float32  

> open "/Users/laura/Documents/RSC/Cartes
> cryo/Cartes3/cryosparc_P197_J792_007_volume_map_sharp.mrc"

Opened cryosparc_P197_J792_007_volume_map_sharp.mrc as #4, grid size
450,450,450, pixel 0.84, shown at level 0.0932, step 2, values float32  

> volume #2 step 1

> volume #3 step 1

> volume #4 step 1

> volume #2 level 0.1866

> volume #3 level 0.1506

> volume #4 level 0.1787

> hide #!3 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.87773,-0.33325,-0.34429,93.421,0.060432,0.78979,-0.6104,88.9,0.47533,0.51496,0.71336,-81.963

> view matrix models
> #1,0.95788,-0.21121,-0.19457,52.225,0.081622,0.84984,-0.52068,68.906,0.27533,0.48287,0.83129,-68.407

> view matrix models
> #1,0.95788,-0.21121,-0.19457,105.92,0.081622,0.84984,-0.52068,130.52,0.27533,0.48287,0.83129,-1.563

> fitmap #1 inMap #2

Fit map cryosparc_P197_J770_map_sharp.mrc in map
cryosparc_P197_J776_005_volume_map_sharp.mrc using 189333 points  
correlation = 0.6319, correlation about mean = 0.1245, overlap = 917.7  
steps = 440, shift = 14.3, angle = 34.9 degrees  
  
Position of cryosparc_P197_J770_map_sharp.mrc (#1) relative to
cryosparc_P197_J776_005_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999906 -0.00135361 0.00019561 63.10057465  
0.00135375 0.99999882 -0.00072958 62.82585820  
-0.00019462 0.00072984 0.99999971 62.78499078  
Axis 0.47073172 0.12586611 0.87325218  
Axis point -37801.53402626 14496.30393359 0.00000000  
Rotation angle (degrees) 0.08881763  
Shift along axis 92.43821875  
  

> show #!3 models

> show #!4 models

> surface dust #1 size 8.4

> select subtract #1

Nothing selected  

> hide #!3 models

> hide #!4 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> surface dust #2 size 8.4

> hide #!2 models

> show #!3 models

> surface dust #3 size 8.4

> show #!4 models

> hide #!3 models

> surface dust #4 size 8.4

> show #!1 models

> show #!2 models

> show #!3 models

> volume #2 level 0.2925

> volume #3 level 0.2119

> open /Users/laura/Downloads/HBlobe_166-ajust(2).pdb

Chain information for HBlobe_166-ajust(2).pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
K | No description available  
  

> open /Users/laura/Downloads/HBlobe_166-ajust(1).pdb

Chain information for HBlobe_166-ajust(1).pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
F | No description available  
G | No description available  
H | No description available  
K | No description available  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> close #6

> open /Users/laura/Downloads/DBLOBE_2805_renumbered(2).pdb

Chain information for DBLOBE_2805_renumbered(2).pdb #6  
---  
Chain | Description  
A | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
K | No description available  
N | No description available  
  

> show #!5 models

> open /Volumes/ibs-equipe-
> petosa/CaRSC_Structure/NB_Lobe/NB_AF_comp_RB_job50v1.pdb

Chain information for NB_AF_comp_RB_job50v1.pdb #7  
---  
Chain | Description  
F | No description available  
G | No description available  
I | No description available  
M | No description available  
  

> hide atoms

> show cartoons

> hide cartoons

> show surfaces

> hide surfaces

> show atoms

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 20974 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> ui tool show XMAS

  
Peptide pair mapping of Xi evidence file:
/Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2).csv  
Unique peptide pairs: 1198 out of 1211  
Unique peptide pairs with pseudobonds: 104  
Pseudobonds are stored in
/Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2)_5,6,7.pb  
Mapping information is stored in
/Users/laura/Downloads/RSC_BS3_msconvert_Xi1.7.6.7_PeptidePairs_xiFDR2.1.5.5(2)_5,6,7.tsv  
Venn diagrams can only be plotted for two or three groups  
/Users/laura/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.  
warnings.warn(msg, FutureWarning)  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1916.60.2.0.0 (iBridge: 20.16.2059.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6.2 (21G320)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 17:16

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PHL 258B6QU:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: UHB1949004141
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openpyxl: 3.1.0
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    seaborn: 0.12.2
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0